Extraction and packaging of the energy

from food stuffs

Why and how we make ATP?

energy

+ O2 → CO2 + H2O + ATP

The sum total of the chemical activities of all cells.

 Bioenergetics and Thermodynamics

Biological energy transductions obeys some

physical laws that govern all other natural process

In this chapter we first review

• The laws of thermodynamics

• The special role of ATP in biological energy

exchanges

. The importance of oxidation-reduction reactions in living cells

• The energetics of electron-transfer reactions

• The electron carriers commonly employed as cofactors of the

enzymes that catalyze these reactions
 What is Bioenergetics?

• The ability or capacity to perform work

• The study of energy in living systems
(environments) and the organisms (plants
and animals) that utilize them

“…..the study of the flow and transformation of

energy in and between living organisms and between
living organisms and their environment”
 Thermodynamics/ Bioenergetics

❖ The study of energy transformations that occur in a

collection of matter is called Thermodynamics.

❖ The Thermodynamics in living organisms is called

Bioenergetics.

❖ In other words, Bioenergetics is the study of energy in

living systems

❖ Living systems = Environments + Organisms

 First & second Laws of Thermodynamics
• First Law: Energy cannot be created or destroyed, but only converted
to other forms.
This means that the amount of energy in the universe is constant

• Second Law: The universe always tend towards increasing disorder: in

all natural processes the entropy of the universe increases
Biological Energy transformations obey the Laws
of Thermodynamics
➢ For any physical or chemical change, the total amount of
energy in the universe remains constant; but it cannot be
created or destroyed

➢ The universe always tends toward increasing disorder: in

all natural processes, the entropy of the universe increases

➢ Living cells and organisms are open system, exchanging

both material and energy with their surroundings

➢ living systems are never at equilibrium with their

surrounding, and the constant transactions between
system and surrounding explain how organisms can create
order within themselves while operating within the second
law of the thermodynamics
 A B
SA SB

HA GA HB
GB

IF:
H = Enthalpy= the total heat of a system
G = Free energy= the amount of usable energy in a
system that can be used to perform a work.
S =Entropy = the amount of disorder in a system. In most
but not all cases it is heat

Then somehow:
∆G= GB-GA
∆H= HB-HA
∆S= SB-SA
 Relationship between energy and entropy

• Both entropy and enthalpy contribute to DG

DG = DH - TDS
(T = degrees Kelvin)
-DG = a spontaneous reaction in the
direction written
+DG = the reaction is not spontaneous
DG = 0 the reaction is at equilibrium
 Bioenergetics and Thermodynamics

Gibbs free energy, G, expresses the amount of energy capable of doing

work during a reaction at constant temperature and pressure. When a reaction
proceeds with the release of free energy (that is, when the system changes so as
to possess less free energy), the free-energy change, G, has a negative value and
the reaction is said to be exergonic. In endergonic reactions, the system gains
free energy and G is positive.

Enthalpy, H, is the heat content of the reacting system. It reflects the number
and kinds of chemical bonds in the reactants and products. When a chemical
reaction releases heat, it is said to be exothermic; the heat content of the products
is less than that of the reactants and H has, by convention, a negative value.
Reacting systems that take up heat from their surroundings are endothermic and
have positive values of H.

Entropy, S, is a quantitative expression for the randomness or disorder in a

system. When the products of a reaction are less complex and more disordered
than the reactants, the reaction is said to proceed with a gain in entropy.
 Gibbs equation

• ∆G = ∆H - T∆S
• Gibbs equation in living organisms
• ∆G = ∆E - T∆S
• The relationship between the value of ∆G and the
spontaneity of a reaction:
• Endergonic Reactions have: ∆G +
• Exergonic Reactions have : ∆G -
• At equilibrium state have: ∆G = 0
 Standard Free-Energy Change
(DGo)
• Reaction free-energy depends upon conditions
• Standard state (DGo) - defined reference conditions
Standard Temperature = 298K (25oC)
Standard Pressure = 1 atmosphere
Standard Solute Concentration = 1.0M
• Standard transformed constant = DGo’
Standard H+ concentration = 10-7 (pH = 7.0)
H2O concentration = 55.5 M
Mg2+ concentration = 1 mM
 Cells require sources of free energy

➢ Cells are isothermal systems that works at essentially constant

temperature and pressure
➢ Heat flow is not the source of energy for cells b/c heat can do work only
when passes to a zone at low temperature
➢ The energy that cells can and must use is free energy, described by the
Gibbs free-energy function G, which predicting the direction of
chemical reaction, their exact equilibrium position and the amount of
work they can in theory perform at constant temperature and
pressure
➢ Heterotrophic cells acquire free energy from nutrient molecules, and
photosynthetic cells acquire it from absorbed solar radiation
➢ Both kind of cells trans formed this free energy into ATP and other
energy-rich compounds capable of providing energy for biological
work at constant temperature
 Standard Free-Energy Change and
Equilibrium Constants
Composition of a reacting system (mixture of chemical reactants and
products) tends to continue changing until equilibrium is reached

For the reaction: aA + bB cC + dD

At equilibrium concentration of reactants & products, rates of forward & reverse
reactions are exactly equal & no further net change occurs in the system

At equilibrium: Keq = [C][D]/[A][B] and

DG reaction = 0

DG reaction = DGo’ reaction +RT ln([C]c[D]d/[A]a[B]b)

DGo’ reaction = -RT ln Keq

 Glucose 1-phosphate glucose 6-phosphate
Phosphoglucomutase

[glucose 6-phosphate] 19mM

Keq= [glucose 1-phosphate] = = 19
1mM

From this value of Keq we can calculate the standard free-energy change:

∆Gº = -- RT ln Keq
= -- (8.315 J/mol K)(298 K)(ln 19)
= --7.3 kJ/mol
Phosphoryl Group Transfers and ATP
➢ Energy cycle in cells
➢ Special role of ATP as the energy currency
➢ Links catabolism and anabolism

It is estimated that each cell is generating &

consuming approximately
10,000,000 molecules of ATP per second
2,16x1022 molecules of ATP
ATP then donating its chemical energy to endergonic processes such
as the synthesis of metabolic intermediates and macromolecules from
smaller precursors

The sum total of the chemical activities of all cells is called Cellular Metabolism

• Anabolic Pathways (Endergonic reactions):

Those that consume energy to build complicated molecules from simpler
compounds such as: Protein, Glycogen & lipid synthesis.

SUN Light energy

Photosynthesis
6CO2 + 6H2O → C6H12O6 + 6O2
(glucose)
• Catabolic Pathways (Exergonic reactions):
Those that release energy by breaking down complex molecules into
simpler compounds such as glycolysis.
Cellular Respiration energy
C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP
(glucose)
➢ This donation of energy from ATP generally involves the covalent participation
of ATP in the reaction that is to be driven, with the eventual result that ATP is
converted to ADP and Pi or, in some reactions, to AMP and 2 Pi

➢ The chemical basis for the large free-energy changes that accompany
hydrolysis of ATP and other high-energy phosphate compounds

➢ In most cases of energy donation by ATP involve group transfer, not simple
hydrolysis of ATP

• Single-step vs multi-step pathways

• A multistep enzyme pathway releases
energy in smaller amounts that can be
used by the cell
 The Free Energy change for ATP
• Energy from oxidation of metabolic fuels is largely
recovered in the form of ATP
• The free energy change for ATP hydrolysis is large and
negative

Components
1. Adenine: Nitrogenous base
2. Ribose: Five carbon sugar
3. Phosphate group: Chain of 3

Phosphate group Adenine

ribose
 Hydrolysis of ATP
electrostatic repulsing
• Hydrolysis, by causing
charge separation (relieves
electrostatic repulsing)

• Pi is stabilized by formation
of a resonance hybrid (same
degree of double bound)

• ADP2- immediately ionizes,

releasing a proton into a
medium of very low (H+)

• Greater degree of solvation

of the products Pi and ADP
solvation relative to ATP
Hydrolysis of ATP
 Hydrolysis of phosphoenolpyruvate (PEP)

Catalyzed by pyruvate kinase, this reaction is followed by spontaneous

tautomerization of the product, pyruvate, tautomerization is not
possible in PEP, and thus the products of hydrolysis are stabilized
relative to reactants. Resonance stabilization of Pi also occurs
 Hydrolysis of 1, 3-bisphosphoglycerate

• The direct product of hydrolysis is 3-phosphoglyceric acid, which has an un -

dissociated carboxylic acid group, but dissociation occurs immediately. This
ionization and the resonance structures, it makes possible stabilize the product
relative to the reactants.
• Resonance stabilization of Pi further contributes to the negative free-energy
change.
 Hydrolysis of phosphocreatine

• Breakage of the P-N bond in phosphocreatine produces creatine,

which is stabilized by formation of a resonance hybrid.
Thioesters: Hydrolysis of acetyl-coenzyme A

• Acetyl-CoA is a thioester
with a large, negative,
standard free energy of
hydrolysis. Thioesters
contain a sulfur atom in
the position occupied by
an oxygen atom in
oxygen esters.
ATP provides energy by group transfers, Not by simple
hydrolysis --- in two steps

• A phosphoryl group is first

transferred from ATP to
glutamate

• The phosphoryl group is

displaced by NH3 and
released as Pi

• ATP can carry energy from

high-energy phosphate
compounds produced by
catabolism to compounds
such as glucose, converting
them into more reactive
species

• ATP thus serves as the

universal energy currency in
all living cells
 Phosphoryl-Group Transfer
Nucleophilic displacement reaction of ATP (nucleophilic displacements)
ATP donates 1). phosphoryl, 2). pyrophosphoryl, and 3). adenylyl groups
Fire flashes: glowing reports of ATP

• From chemical energy into light energy.

• An pyrophosphate cleavage of ATP to

form luciferyl adenylate. In the presence
of O2 and luciferase, the luciferin
undergoes a multiple step oxidative
decarboxylation to oxyluciferin and
accompanied by remission of light.
ATP as energy currency in many biochemistry reactions
• Inorganic pyrophosphatase hydrolyed the PPi to two Pi,
releasing 19 KJ/mol.
• Activation of a fatty acid --- either for energy-yielding
oxidation or for use in the synthesis of more complex
lipids: is attached to the carrier coenzyme A.
• Assembly of informational macromolecules – RNA .
• ATP energizes active transport and muscle contraction.
• Transphosphorylations between Nucleotides occur in all
cell type (NTP—NDP: Nucleoside diphosphate kinase or
Adenylate kinase or Creatine kinase,
• Inorganic polyphosphate is a potential phosphoryl
group donor (polyphosphate kinase —energy reservoir)

Nucleoside diphosphate kinase

Adenylate kinase

Creatine kinase
 Ping-Pong Mechanism of Nucleoside diphosphate

The enzyme binds its first substrate (ATP), and a phosphoryl group is
transferred to the side chain of a His residue. ADP departs, and another
nucleoside diphosphate replace it, and this is converted to the
corresponding triphosphate by transfer of the phosphoryl group from the
phosphohistidine residue.
SUMMARY

➢ ATP is the chemical link between catabolism and anabolism. It is the energy
currency of the living cell. The exergonic conversion of ATP to ADP and Pi, or to
AMP and PPi, is coupled to many endergonic reactions and processes.
➢ Direct hydrolysis of ATP is the source of energy in the conformational changes
that produce muscle contraction but, in general, it is not ATP hydrolysis but the
transfer of a phosphoryl, pyrophosphoryl, or adenylyl group from ATP to a substrate
or enzyme molecule that couples the energy of ATP breakdown to endergonic
transformations of substrates.
➢ Through these group transfer reactions, ATP provides the energy for anabolic
reactions, including the synthesis of informational molecules, and for the transport
of molecules and ions across membranes against concentration gradients and
electrical potential gradients.
➢ Cells contain other metabolites with large, negative, free energies of hydrolysis,
including phosphoenolpyruvate, 1,3-bisphosphoglycerate, and phosphocreatine.
These high-energy compounds, like ATP, have a high phosphoryl group transfer
potential; they are good donors of the phosphoryl group. Thioesters also have high
free energies of hydrolysis.
➢ Inorganic polyphosphate, present in all cells, may serve as a reservoir of
phosphoryl groups with high group transfer potential.
 Biological
Oxidation- Reduction
Reactions
Most energy from fuel (food) obtained through
oxidative processes:

• oxidation :
* Gain of Oxygen
* Loss of Hydrogen
* Loss of electrons
• Reduction:
* Gain of Hydrogen
* Gain of electron
* Loss of Oxygen

Oxidation and reduction must occur simultaneously

 The flow of electrons can do Biological work
What is Electromotive force (emf)?
• A battery (as source of electron) containing two chemical
species different in electron affinity
• Electrical wires provide a pathway for electron flow through
the motor from one chemical species tom the other
• The driving force cause spontaneous electron flow between
two chemical species differ in electron affinity is called emf
• emf is proportional to the difference in electron affinity
Biological circuit in living cells
• Relatively reduced compound glucose act as electron source
enzymatically oxidized
• Released electron flow through a series of electron-carrier
intermediates to O2 having higher affinity for electron than the
intermediate so reaction is exergonic
• The resulting emf provide energy to variety of energy
transducers like enzymes etc.
 Oxidation-reduction reactions

Conjugated redox pair: Fe2+ (electron donor), and Fe3+ (electron acceptor)
oxidation of a reducing sugar (an aldehyde or ketone) by cupric ion
Biological oxidations often involved dehydrogenation

• The Carbon in living cells exist in a range of

oxidation states

• When C share an electron pair with another

atom. The sharing is unequal in favor of the
more electronegative atom (H < C < S < N < O)

• Electrons transfer in 4 ways: as

• e-
• hydrogen atoms (H)
• hydride ion (H-)
• combination with oxygen

• Reducing equivalent: a single electron

equivalent participating in an oxidation-
reduction reaction
• biological oxidations as two reducing
equivalents passing from substrate to oxygen
 E = Reduction Potential (Redox)

Redox potential measures of the tendency of oxidant to

gain electrons, to become reduced, it is a potential
energy

Electrons move from compounds with lower reduction

potential (more negative ) to compounds with higher
reduction potential ( more positive)

Reductant  oxidant + e-

Oxidant + e-  reductant
 Reduced Coenzymes Conserve Energy from
Biological Oxidations

• Amino acids, monosaccharides and lipids are oxidized in the catabolic

pathways
• Oxidizing agent - accepts electrons, is reduced
• Reducing agent - loses electrons, is oxidized
• Oxidation of one molecule must be coupled with the reduction of another
molecule

Ared + Box Aox + Bred

 Free-Energy Change Is Related
to Reduction Potential

• The reduction potential of a reducing agent is a measure of its

thermodynamic reactivity
• The electromotive force is the measured potential difference between two
half-cells
• Standard reduction potential is for hydrogen:

Eo = H + + e - ½ H2
Measurement of the standard reduction potential (E’o) of a redox pair

The ultimate reference half-cell is the

hydrogen electrode, at pH 0. The
electromotive force (emf) of this electrode
is designated 0.00 V. At pH 7 in the test
cell, E for the hydrogen electrode is
0.414 V.

Electrons tend to flow through the

external circuit from the half-cell of lower
standard reduction potential to the half-
cell of higher standard reduction potential.
By convention, the half-cell with the
stronger tendency to acquire electrons is
assigned a positive value of E.
 Standard reduction potentials and free
energy

• Relationship between standard free-energy

change and the standard reduction potential:

DGo’ = -nFDEo’

n = # electrons transferred
F = Faraday constant (96.48 kJ V-1)
DEo’ = Eo’electron acceptor - Eo’electron donor
Coenzymes and proteins as electron carriers

• NAD and NADP+

• FMN and FAD
• Ubiquinone and plastoquinone
• Iron sulfur proteins and cytochromes
 NADH and NADPH act with dehydrogenases
as water soluble electron carriers

H: - + H+

• From vitamin niacin (source of

the nicotinamide)
• Accepts a hydride ion and
transformed into the reduced
form
• NADH absorb at 340 nm.
• NAD generally functions in
oxidations as part of a catabolic
reaction, NADPH is the usual
coenzyme in reduction as part
of anabolic reaction
• Rossmann fold: most dehydro-
genase that use NAD or NADP
bind the cofactor in the
conserved protein domain
Structure of oxidized and reduced FAD and FMN
• Flavin Nucleotides are tightly bound
in flavoproteins, accepts 1 or 2
electrons
• Oxidized flavoproteins have an
absorption maximum near 570 nm;
reduced forms shifts to about 450 nm.
• Do not transfer electron by diffusing
from one enzyme to another. Provide
a means by which the flavoprotein
can temporarily hold electron wile it
catalyzes electron transfer from a
reduce substrate to an electron
acceptor
• Variability in the standard reduction
potential of the bound flavin
nucleotide
• Complex -may bound Fe or Mo